Merge branch 'master' of https://github.com/osolari/osolari.github.io

.github/workflows/import-publoications.yml

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+# Hugo Blox GitHub Action to convert Bibtex publications to Markdown-based webpages
+name: Import Publications From Bibtex
+
+# Require permission to create a PR
+permissions:
+  contents: write
+  pull-requests: write
+
+# Run workflow when a `.bib` file is added or updated in the `data/` folder
+on:
+  push:
+    branches: ['main']
+    paths: ['publications.bib']
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  hugoblox:
+    if: github.repository_owner != 'HugoBlox'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout the repo
+        uses: actions/checkout@v3
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.12"
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install academic==0.10.0
+      - name: Run Academic (Bibtex To Markdown Converter)
+        # Check `.bib` file exists for case when action runs on `.bib` deletion
+        # Note GH only provides hashFiles func in `steps.if` context, not `jobs.if` context
+        if: ${{ hashFiles('publications.bib') != '' }}
+        run: academic import publications.bib content/publication/ --compact
+      - name: Create Pull Request
+        # Set ID for `Check outputs` stage
+        id: cpr
+        uses: peter-evans/create-pull-request@v5
+        with:
+          commit-message: 'content: import publications from Bibtex'
+          title: Hugo Blox Builder - Import latest publications
+          body: |
+            Import the latest publications from `publications.bib` to `content/publication/`.
+            将最新的出版物从`publications.bib`导入到`content/publication/`。
+            [View Documentation](https://github.com/GetRD/academic-file-converter)
+          base: main
+          labels: automated-pr, content
+          branch: hugoblox-import-publications
+          delete-branch: true
+      - name: Check outputs
+        if: ${{ steps.cpr.outputs.pull-request-number }}
+        run: |
+          echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"
+          echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"

.github/workflows/publish.yml

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+name: Deploy website to GitHub Pages
+
+env:
+  WC_HUGO_VERSION: '0.136.5'
+
+on:
+  # Trigger the workflow every time you push to the `main` branch
+  push:
+    branches: ["main"]
+  # Allows you to run this workflow manually from the Actions tab on GitHub.
+  workflow_dispatch:
+
+# Provide permission to clone the repo and deploy it to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  # Build website
+  build:
+    if: github.repository_owner != 'HugoBlox'
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+          # Fetch history for Hugo's .GitInfo and .Lastmod
+        fetch-depth: 0
+    - name: Setup Hugo
+      uses: peaceiris/actions-hugo@v2
+      with:
+        hugo-version: ${{ env.WC_HUGO_VERSION }}
+        extended: true
+    - uses: actions/cache@v3
+      with:
+        path: /tmp/hugo_cache_runner/
+        key: ${{ runner.os }}-hugomod-${{ hashFiles('**/go.mod') }}
+        restore-keys: |
+          ${{ runner.os }}-hugomod-
+    - name: Setup Pages
+      id: pages
+      uses: actions/configure-pages@v3
+    - name: Build with Hugo
+      env:
+        HUGO_ENVIRONMENT: production
+      run: |
+        echo "Hugo Cache Dir: $(hugo config | grep cachedir)"
+        hugo --minify --baseURL "${{ steps.pages.outputs.base_url }}/"
+    - name: Generate Pagefind search index
+      run: npx pagefind --site "public"
+    - name: Upload artifact
+      uses: actions/upload-pages-artifact@v2
+      with:
+        path: ./public
+
+  # Deploy website to GitHub Pages hosting
+  deploy:
+    if: github.repository_owner != 'HugoBlox'
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+    - name: Deploy to GitHub Pages
+      id: deployment
+      uses: actions/deploy-pages@v2

.github/workflows/updater-wip.yml

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+name: Updater (WIP)
+
+on:
+  schedule:
+    - cron: 0 0 * * 0
+  # Allows you to run this workflow manually from the Actions tab on GitHub.
+  workflow_dispatch:
+
+# Provide permission to clone the repo and deploy it to GitHub Pages
+permissions:
+  contents: write
+
+jobs:
+  update:
+    if: github.repository_owner == 'HugoBlox'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: HugoBlox/gh-action-updater@v1
+        with:
+          feed-url: https://hugoblox.com/rss.xml
+          readme-section: news
+          branch: main

publications.bib

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+@article{orsini2016daphnia,
+  title={Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors},
+  author={Orsini, Luisa and Gilbert, Donald and Podicheti, Ram and Jansen, Mieke and Brown, James B and Solari, Omid Shams and Spanier, Katina I and Colbourne, John K and Rusch, Douglas B and Decaestecker, Ellen and others},
+  journal={Scientific data},
+  volume={3},
+  pages={160030},
+  year={2016},
+  publisher={Nature Publishing Group}
+}
+
+@article{orsini2018early,
+  title={Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes},
+  author={Orsini, Luisa and Brown, James B and Shams Solari, Omid and Li, Dong and He, Shan and Podicheti, Ram and Stoiber, Marcus H and Spanier, Katina I and Gilbert, Donald and Jansen, Mieke and others},
+  journal={Molecular Ecology},
+  volume={27},
+  number={4},
+  pages={886--897},
+  year={2018}
+}
+
+@article{arbel2019exploiting,
+  title={Exploiting regulatory heterogeneity to systematically identify enhancers with high accuracy},
+  author={Arbel, Hamutal and Basu, Sumanta and Fisher, William W and Hammonds, Ann S and Wan, Kenneth H and Park, Soo and Weiszmann, Richard and Booth, Benjamin W and Keranen, Soile V and Henriquez, Clara and others},
+  journal={Proceedings of the National Academy of Sciences},
+  volume={116},
+  number={3},
+  pages={900--908},
+  year={2019},
+  publisher={National Academy of Sciences}
+}
+
+@article{kvist2018pattern,
+  title={Pattern of DNA methylation in Daphnia: evolutionary perspective},
+  author={Kvist, Jouni and Gon{\c{c}}alves Athan{\`a}sio, Camila and Shams Solari, Omid and Brown, James B and Colbourne, John K and Pfrender, Michael E and Mirbahai, Leda},
+  journal={Genome biology and evolution},
+  volume={10},
+  number={8},
+  pages={1988--2007},
+  year={2018},
+  publisher={Oxford University Press}
+}
+
+@article{pourbabaee2019large,
+  title={Large Deviations of Linear Models with Regularly-Varying Tails: Asymptotics and Efficient Estimation},
+  author={Pourbabaee, Farzad and Solari, Omid Shams},
+  journal={arxiv},
+  volume={1903},
+  number={12299},
+  pages={24},
+  year={2019}
+}
+
+@article{solari2019sparse,
+  title={Sparse canonical correlation analysis via concave minimization},
+  author={Solari, Omid S and Brown, James B and Bickel, Peter J},
+  journal={arXiv preprint arXiv:1909.07947},
+  year={2019}
+}
+
+@article{solari2019bloccs,
+  title={BLOCCS: Block Sparse Canonical Correlation Analysis With Application To Interpretable Omics Integration},
+  author={Solari, Omid Shams and Safavi, Rojin and Brown, James B},
+  journal={arXiv preprint arXiv:1909.07944},
+  year={2019}
+}
+
+@article{shams2019large,
+  title={Large-Scale Interpretable Multi-View Learning for Very High-Dimensional Problems with},
+  author={Shams Solari, Omid},
+  year={2019}
+}
+
+@article{shams2019bloccs,
+  title={BLOCCS: Block Sparse Canonical Correlation Analysis With Application To Interpretable Omics Integration},
+  author={Shams Solari, Omid and Safavi, Rojin and Brown, James B},
+  journal={arXiv e-prints},
+  pages={arXiv--1909},
+  year={2019}
+}
+
+@phdthesis{shams2019large,
+  title={Large-Scale Interpretable Multi-View Learning for Very High-Dimensional Problems with Application to Multi-Omic Data},
+  author={Shams Solari, Omid},
+  year={2019},
+  school={UC Berkeley}
+}
+
+@phdthesis{solari2019large,
+  title={Large-Scale Interpretable Multi-View Learning for Very High-Dimensional Problems with Application to Multi-Omic Data},
+  author={Solari, Omid Shams},
+  year={2019},
+  school={University of California, Berkeley}
+}
+
+@article{kvistpattern,
+  title={Pattern of DNA methylation in Daphnia},
+  author={Kvist, Jouni and Athan{\`a}sio, Camila Gon{\c{c}}alves and Solari, Omid Shams and Brown, James and Colbourne, John and Pfrender, Michael E and Mirbahai, Leda}
+}
+
+@article{pourbabaee2019large,
+  title={Large Deviations of Factor Models with Regularly-Varying Tails: Asymptotics and Efficient Estimation},
+  author={Pourbabaee, Farzad and Solari, Omid Shams},
+  journal={arXiv preprint arXiv:1903.12299},
+  year={2019}
+}
+
+@article{pourbabaee2022tail,
+  title={Tail Probability Estimation of Factor Models with Regularly-Varying Tails: Asymptotics and Efficient Estimation},
+  author={Pourbabaee, Farzad and Shams Solari, Omid},
+  journal={Available at SSRN 4078304},
+  year={2022}
+}
+
+@article{gafni2021cell,
+  title={Cell-free DNA fragments inform epigenomic mechanisms for early detection of breast cancer},
+  author={Gafni, Erik and Harvey, Adam and Jaroszewicz, Artur and Solari, Omid Shams and Landolin, Jane and Barbirou, Mouadh and Miller, Amanda and Tonellato, Peter J and Kundaje, Anshul and Jeffrey, Stefanie S and others},
+  journal={Cancer Research},
+  volume={81},
+  number={13\_Supplement},
+  pages={2105--2105},
+  year={2021},
+  publisher={AACR}
+}
+
+@misc{myer2024comparison,
+  title={Comparison of colorectal cancer (CRC) characteristics across genetic ancestries: Implications for early cancer detection (ECD).},
+  author={Myer, Parvathi and Srinivasan, Preethi and Bristow, Sara L and Krinshpun, Shifra and Solari, Omid and Aushev, Vasily N and Jurdi, Adham A and Liu, Minetta C and Mitchell, Breeana L and Aleshin, Alexey and others},
+  year={2024},
+  publisher={American Society of Clinical Oncology}
+}
+
+@misc{solari2024comprehensive,
+  title={Comprehensive analysis of differentially methylated regions in colorectal cancer (CRC).},
+  author={Solari, Omid and Constantin, Tudor and Jiang, Yuqian and Chan, Wengching and Tunc, Ilker and Srinivasan, Preethi and Kordi, Misagh and Santaguida, Marianne and Mitchell, Breeana L and Aleshin, Alexey and others},
+  year={2024},
+  publisher={American Society of Clinical Oncology}
+}
+
+@article{srinivasan2024circulating,
+  title={Circulating differential methylation allele fraction (DMAF) strongly correlates with circulating tumor DNA (ctDNA) variant allele fraction (VAF)},
+  author={Srinivasan, Preethi and Chen, Tzu-Chun and Haghshenas, Ehsan and Kordi, Misagh and Tunc, Ilker and Chan, Wenching and Solari, Omid Shams and Babiarz, Joshua and Nakamura, Yoshiaki and Yoshino, Takayuki and others},
+  journal={Cancer Research},
+  volume={84},
+  number={6\_Supplement},
+  pages={2409--2409},
+  year={2024},
+  publisher={The American Association for Cancer Research}
+}
+
+@article{myer2024sa1175,
+  title={Sa1175 COMPARISON OF COLORECTAL CANCER (CRC) CHARACTERISTICS ACROSS GENETIC ANCESTRIES: IMPLICATIONS FOR EARLY CANCER DETECTION},
+  author={Myer, Parvathi A and Srinivasan, Preethi and Bristow, Sara L and Krinshpun, Shifra and Solari, Omid Shams and Aushev, Vasily N and Jurdi, Adham and Liu, Minetta C and Mitchell, Breeana L and Aleshin, Alexey and others},
+  journal={Gastroenterology},
+  volume={166},
+  number={5},
+  pages={S--373},
+  year={2024},
+  publisher={WB Saunders}
+}